By way of background, a number of industries are affected by regulations relating to water treatment, such as ballast water treatment systems (“BWTS”) on ships and the like. Such regulations require that microorganisms be effectively rendered non-viable or non-living by the BWTS before such water is returned to the ocean or other body of water. Generally speaking, Zooplankton in the size range of approximately 10 to 50 microns or larger can be the “indicator” microorganism used to determine the effectiveness of treatment. Phytoplankton below 50 microns has also been employed as the indicator organism. To date, monitoring the effectiveness of such BWTS has largely been handled through samples submitted to a lab, there most often involving human examination under a microscope, and the samples themselves being obtained “off-line” as in a collection tank and then having a delay from the sample acquisition event to any manipulation or evaluation of the sample. As such, these laboratory approaches to sample acquisition and compliance assessment have numerous shortcomings in terms of accuracy, speed, and cost. Similarly, flow cytometry systems can offer relatively higher throughput, but not necessarily for real time direct enumeration of live vs dead zooplankton levels, due to a significant amount of man-in-the-loop sample preparation. Fundamentally, neither such prior art approaches provide a mechanism for sorting living organisms from non-living or inorganic matter within the sample as part of the acquisition system or otherwise in an automated form in “real time” or through “on-line” sampling from a fluid flow. The present invention improves and renders deployable the sample acquisition process in meeting these needs and provides further advantages over prior art sampling systems and approaches. The subject invention, though again in the context of BWTS compliance testing, may be practiced in a wide array of contexts and so is not limited to the exemplary BWTS context (for example, ocean, lake, river and stream testing as well as air or other fluid testing). Thus, while “water” is discussed throughout as the sampled fluid, it is to be understood that the invention is not so limited and other fluids may be sampled as well, again depending on the context.